James and the Giant Corn Genetics: Studying the Source Code of Nature

December 1, 2009

One of the Joys of Comparative Genomics

Filed under: Computers and Coding,research stories — Tags: , — James @ 1:26 pm

I was originally scheduled to fly home yesterday, but was forced to extend my stay by unfortunate chain of events that (among other things) has resulted with me swearing off contact lenses for the foreseeable future.

If I worked with arabidopsis or brachypodium, I’d probably have plants flowering this week that I’d be missing. Without the chance to make the crosses I needed to continue my research I might be set back a month or more while I waiting for new plants to grow. If I was mostly doing wet lab work, I wouldn’t fall as far behind assuming I’d gotten all my projects properly refrigerated or frozen before leaving for Thanksgiving, but the whole week I was gone would still be a complete loss.

Fortunately, I now study comparative genomics, which means, while I won’t get as much done this week as I normally would have, I’m definitely going to continue working. I’ve already shown off my workstation in the lab.

And here is where I’ll be working most of this week.


I’ve been advised, by people who’ve been doing a lot longer than I have, that working on a laptop long-term is a great way to burn out your hands (carpel tunnel), but for a week it’s no big deal. I can get more work done from here, thousands of miles away, than from an apartment a few blocked from the job, because the faster internet connection means I’m better able to access my own workstation (the first computer pictured), two of the my lab’s servers, and even a Linux box I left running in my apartment, all of which was using for different parts on my work on Monday.

If you look closely you’ll also notice one other difference between the permanent and temporary digs. Just for this week, I have a window!

July 12, 2008

The New PC

Filed under: Electronics — Tags: , , , — James @ 10:49 pm

As a computer geek I need a computer that’s online 24/7. This uses a lot of electricity which A. costs money B. Makes the environmentalists in my life hate me.

Now I could choose between my computerized lifestyle and ever dating another environmentalist (GMO issue aside). Or I could cut my power usage by building a second (super efficient) PC so I can turn off the powerful, power hungry, machine I use for the computational heavy lifting whenever I don’t need it. Guess which option I chose? 😉

Now for the second challenge, my budget for my entire energy efficient computer: $150 (Note that the cheapest computer listed on the best buy website as of this writing is $280.)

  • Processor: Celeron 430L 1.8GHz – Maximum power usage of 35 watts. A standard CPU draws 90 watts, enthusiast CPUs 125 watts or more.
  • Motherboard:MSI P6NGM-FD – On-motherboard graphics save energy vs. a discrete graphics card, and I’ll barely ever even connect a monitor.
  • Memory: 1 Gig G.Skill DDR2 800 – not much to say here, it’s the right speed, it’s cheap.
  • Case: Rosewill R102-P-BK – MicroATX case, cheap, enough room for my hard drives.
  • Operating system: Ubuntu Linux – It’s free, and on this budget I need that.
  • Hard drive: I can use my current hard drives
  • Power Supply: Left over from a system upgrade. Aftermarket power supplies are more efficient. Cheap ones have conversion efficiencies as low as 60-70%

All the components arrived from new egg the middle of last week. Initially set up goes well:
Linux Box Step 2
But then problems arise. Ubuntu is on a DVD. The only DVD drive I own is already installed in my current PC and I can’t remember how to get it out. The solution? Siamese computers!
Computer Life Support
By flipping the new computer upside down and running IDE and power cables between the two I can manage the linux installation!
And now, a mere 72 hours later, I have a working computer!

Ubuntu has many positive qualities. User customization (without spending hours on google and the absolute beginners ubuntu forums) is not one of them.

Anyway the end result: The computer I used to run 24/7 drew 110-120 watts idle. The new one just under 50. For $150 I’ve reduced power consumption by 43-50 kilowatt hours a month. At an electricity rate of 12 cents a kW/h, bringing this new computer online will save 70 bucks a year in electricity and pay for itself in 25 months.

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